List of works - Yi Zheng

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit

scientific article published on 9 November 2015

A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters

scientific article

A dynamic evolutionary and functional landscape of plant phased small interfering RNAs.

scientific article published on 16 May 2015

A novel method of transcriptome interpretation reveals a quantitative suppressive effect on tomato immune signaling by two domains in a single pathogen effector protein.

scientific article

A tomato phloem-mobile protein regulates the shoot-to-root ratio by mediating the auxin response in distant organs.

scientific article

An NAC transcription factor controls ethylene-regulated cell expansion in flower petals

scientific article

Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon.

scientific article

Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles ⬇️

scientific article published on September 21, 2011

Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development

scientific article published on 16 June 2015

Comparative Transcriptomes Analysis of Red- and White-Fleshed Apples in an F1 Population of Malus sieversii f. niedzwetzkyana Crossed with M. domestica 'Fuji'.

scientific article

Comparative genomics reveals candidate carotenoid pathway regulators of ripening watermelon fruit.

scientific article

Complete Genome Sequence of Southern tomato virus Identified in China Using Next-Generation Sequencing

scientific article

Complete Genome Sequence of Southern tomato virus Naturally Infecting Tomatoes in Bangladesh

scientific article

Complete Genome Sequence of a Tomato-Infecting Tomato Mottle Mosaic Virus in New York

scientific article

Complete Genome Sequence of an Emerging Melon Necrotic Spot Virus Isolate Infecting Greenhouse Cucumber in North America

scientific article published on 16 July 2015

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development.

scientific article published on 22 June 2015

Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.)

scientific article (publication date: 21 October 2013)

Comprehensive transcriptome analyses reveal tomato plant responses to tobacco rattle virus-based gene silencing vectors

scientific article published on 29 August 2017

De novo and comparative transcriptome analysis of cultivated and wild spinach

scientific article

Distinct Mechanisms of the ORANGE Protein in Controlling Carotenoid Flux

scientific article (publication date: 2017)

Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

scientific article

Elucidation of the Mechanisms of Long-Distance mRNA Movement in a Nicotiana benthamiana/Tomato Heterograft System

scientific article published on 02 May 2018

Ethylene suppresses tomato (Solanum lycopersicum) fruit set through modification of gibberellin metabolism.

scientific article

Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family

scientific article published on 07 February 2014

First complete genome sequence of an emerging cucumber green mottle mosaic virus isolate in north america

scientific article published on 7 May 2015

Genome-wide Identification and Expression Analysis of the CDPK Gene Family in Grape, Vitis spp.

scientific article published on 30 June 2015

Genome-wide identification and analysis of the SBP-box family genes in apple (Malus × domestica Borkh.).

scientific article published on 25 May 2013

Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily in apple (Malus × domestica Borkh.).

scientific article published on 6 August 2013

Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape.

scientific article

Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd

High-Throughput Illumina Strand-Specific RNA Sequencing Library Preparation ⬇️

scientific article published on August 1, 2011

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening.

scientific article

HortGenome Search Engine, a universal genomic search engine for horticultural crops

scientific article published in 2024

Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum

scientific article published on 26 November 2012

Integrative analysis of miRNA and mRNA profiles in response to ethylene in rose petals during flower opening.

scientific article

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics

scientific article published on 01 August 2020

Modulation of RNA polymerase II phosphorylation downstream of pathogen perception orchestrates plant immunity

scientific article published on 26 November 2014

RadishBase: a database for genomics and genetics of radish.

scientific article published on 13 December 2012

RhNAC2 and RhEXPA4 are involved in the regulation of dehydration tolerance during the expansion of rose petals.

scientific article

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening.

scientific article published on 27 January 2013

Suppressing Sorbitol Synthesis Substantially Alters the Global Expression Profile of Stress Response Genes in Apple (Malus domestica) Leaves

scientific article published on 15 June 2015

TAL effector driven induction of a SWEET gene confers susceptibility to bacterial blight of cotton.

scientific article

The Arabidopsis SAFEGUARD1 suppresses singlet oxygen-induced stress responses by protecting grana margins

scientific article published on 11 March 2020

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

scientific article published on 25 November 2012

Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics

scientific article

Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening

scientific article published on 7 February 2014

Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana

scientific article published in Scientific Reports

Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins

scientific article

Transcriptomic and functional analysis of cucumber (Cucumis sativus L.) fruit phloem during early development

scientific article published on 17 October 2018

Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity.

scientific article

List of works by Yi Zheng

A bulk segregant transcriptome analysis reveals metabolic and cellular processes associated with Orange allelic variation and fruit β-carotene accumulation in melon fruit

A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters

A dynamic evolutionary and functional landscape of plant phased small interfering RNAs.

A novel method of transcriptome interpretation reveals a quantitative suppressive effect on tomato immune signaling by two domains in a single pathogen effector protein.

A tomato phloem-mobile protein regulates the shoot-to-root ratio by mediating the auxin response in distant organs.

An NAC transcription factor controls ethylene-regulated cell expansion in flower petals

Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon.

Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles ⬇️

Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development

Comparative Transcriptomes Analysis of Red- and White-Fleshed Apples in an F1 Population of Malus sieversii f. niedzwetzkyana Crossed with M. domestica 'Fuji'.

Comparative genomics reveals candidate carotenoid pathway regulators of ripening watermelon fruit.

Complete Genome Sequence of Southern tomato virus Identified in China Using Next-Generation Sequencing

Complete Genome Sequence of Southern tomato virus Naturally Infecting Tomatoes in Bangladesh

Complete Genome Sequence of a Tomato-Infecting Tomato Mottle Mosaic Virus in New York

Complete Genome Sequence of an Emerging Melon Necrotic Spot Virus Isolate Infecting Greenhouse Cucumber in North America

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development.

Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.)

Comprehensive transcriptome analyses reveal tomato plant responses to tobacco rattle virus-based gene silencing vectors

De novo and comparative transcriptome analysis of cultivated and wild spinach

Distinct Mechanisms of the ORANGE Protein in Controlling Carotenoid Flux

Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

Elucidation of the Mechanisms of Long-Distance mRNA Movement in a Nicotiana benthamiana/Tomato Heterograft System

Ethylene suppresses tomato (Solanum lycopersicum) fruit set through modification of gibberellin metabolism.

Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family

First complete genome sequence of an emerging cucumber green mottle mosaic virus isolate in north america

Genome-wide Identification and Expression Analysis of the CDPK Gene Family in Grape, Vitis spp.

Genome-wide identification and analysis of the SBP-box family genes in apple (Malus × domestica Borkh.).

Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily in apple (Malus × domestica Borkh.).

Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape.

Genomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd

High-Throughput Illumina Strand-Specific RNA Sequencing Library Preparation ⬇️

High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening.

HortGenome Search Engine, a universal genomic search engine for horticultural crops

Incomplete transfer of accessory loci influencing SbMATE expression underlies genetic background effects for aluminum tolerance in sorghum

Integrative analysis of miRNA and mRNA profiles in response to ethylene in rose petals during flower opening.

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics

Modulation of RNA polymerase II phosphorylation downstream of pathogen perception orchestrates plant immunity

RadishBase: a database for genomics and genetics of radish.

RhNAC2 and RhEXPA4 are involved in the regulation of dehydration tolerance during the expansion of rose petals.

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening.

Suppressing Sorbitol Synthesis Substantially Alters the Global Expression Profile of Stress Response Genes in Apple (Malus domestica) Leaves

TAL effector driven induction of a SWEET gene confers susceptibility to bacterial blight of cotton.

The Arabidopsis SAFEGUARD1 suppresses singlet oxygen-induced stress responses by protecting grana margins

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics

Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening

Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana

Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins

Transcriptomic and functional analysis of cucumber (Cucumis sativus L.) fruit phloem during early development

Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity.